I understand that Carbon, Hydrogen, Oxygen, and Nitrogen are the source of a lot of great cheap chemistry and I understand why aliens could be made out of those elements. I don't understand though why they would use amino acid polymers, it seems to be an obtuse and awkward way of getting things done.

Is there something special about amino acids that necessitate their use by life? Or is Protein something cooked into our make-up because of the initial conditions of our abiogenesis?

$\begingroup$Aminoacids are an awesome way of getting things done, I don't get why you think its obtuse and awkward. On the other hand if something was completely different from us is entirely possible they could use other methods.$\endgroup$
– Erik vanDorenFeb 19 '16 at 13:13

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$\begingroup$"Proven" is probably not the right word but for the RNA/DNA/protein- based cellular life that we are used to they seem to be necessary.$\endgroup$
– King-InkFeb 19 '16 at 13:32

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$\begingroup$Amino acids are incredibly versatile. We don't know whether some other class of molecule might also be capable of building everything from hair and sinews to enzymes. The more obvious question is whether there is anything special about the twenty-two amino acids (out of thousands) that life uses here. I'd guess that elsewhere, many of the building blocks are amino acids not known to nature on earth and that 22 is not a magic number.$\endgroup$
– nigel222Feb 19 '16 at 18:13

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$\begingroup$What's interesting is that amino acids form spontaneously, and are ubiquitous, even in space clouds. And nothing else suitable has been found, let alone is laying around ready to use.$\endgroup$
– JDługoszFeb 19 '16 at 18:18

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$\begingroup$You have "xenobilogy" tagged which means: no. Not all live needs protein. Only that life that we know of$\endgroup$
– BlueWizardFeb 25 '16 at 5:55

6 Answers
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The life, as self-reproducing entity, could exist in wide range of forms. You only need to create appropriate environment for self-organizing forms. For example, computer viruses could be called a lifeform entity because they are self-reproducing. Self-repairing and reproducing mechanisms can be a lifeform too. However, not every thing that reproduce itself can be called a lifeform. A form of crystal cell can spread out in a mineral substratum but we could not call it a lifeform. But who knows? Tin pest acts like a disease and a whole armies were defeated because their tin buttons were scattered. In other hand, the spread of prion infection is very similar to a moving crystal form (healthy proteins just change their shape and aggregate like a crystal) but scientists call them a lifeform.

So my answer is, while a formal lifeform could be very different, aliens will be made of proteins with high probability, despite the use of equipment

I think it is more likely that the amino acid based proteins we use today are not the only way to go, but something very similar might be used on other planets. The niche proteins fit are very obvious. They are a way to turn a 1d stream of data from the DNA into a complex 3d molecule. They are our 3d printer of choice.

Could there be other 3d printers? Sure. In fact, I'd really enjoy getting to study them. Why is it so ubiquitous here, well, when you have a hammer, everything looks like a nail. Proteins did their job so well that it made sense to use them for a vast majority of tasks, only turning to harder to manufacture non-protein compounds when needed.

So perhaps the aphorism needs to be extended. If you have a hammer, everything starts looking like a nail. If you have a 3d printer, well...

$\begingroup$This is a nice insight into why amino acids/proteins look like a good choice, and why they might be hard to replace (maybe mention RNA World hypothesis here, as alternative and why considered not as good?). But I am a bit lost about the point of the last paragraph (and the accompanying picture - I understand what it is, but not the point you are trying to make or how it relates to the question, other than a digression from answering the question)$\endgroup$
– Neil SlaterFeb 19 '16 at 22:40

$\begingroup$@NeilSlater If I suggest that other approaches might be feasible, the natural question is "why don't we see them on Earth today?" If we had invested a few million years into proteins, we may start only looking for protein based solutions, even if another material could have done it a bit better. We may have simply stopped looking for alternative approaches$\endgroup$
– Cort AmmonFeb 20 '16 at 0:22

$\begingroup$OK, so it answers "Or is Protein something cooked into our make-up because of the initial conditions of our abiogenesis?" - I lost that link to the question whilst reading, I'm not sure if that's just me, or something about the phrasing in the answer threw me.$\endgroup$
– Neil SlaterFeb 20 '16 at 8:39

The basic Chemistry for forming life means that on a basic level, sugars always form before amino acids.

So let’s imagine a planet where there is a: very little nitrogen gas, b: primal ammonia is absent, c: not enough hydrogen found in atmosphere, or d: have a temperature high enough to turn amino acids into tar.

What you get from this conditions are mostly saccirides, or basically sugars, and some other things like fatty acids. And a lot of different aromatics, nucleobases and so on.

What you get is an RNA world where things like ribosomes never formed.
Sugars and aromatics have different stereoisomers, and the one thing that makes sugar special is that different stereoisomers form hydrogen bonds differently: an OH group that is above the sugar ring can only form a hydrogen bond with a carbonyl group on an aldehyde that is under the ring, and an OH group on a phenol can only form a hydrogen bond with an aldehyde or quinone but not a carboxylic acid, etc.

Binding phosphate you get rna, nucleobase or naphthalene or sugars attached to some other sugar bound by phosphodiester bonds, which can be made into different configurations by base paring or the alternatives of base paring, replica table by the same process.

The thing that rna can do, is that they are both carrier of information and catalyst of biological processes: an alcohol dehydrogenase ribozyme that uses zinc and NADH is not so different than it’s protein counterpart, a rna polymerase ribozyme works similiarily with the real thing and the ribosome itself is also a ribozyme.

Now, phosphate have 3 bonds to it, and only two are used in the actual process of rna polymerization. The third bond is empty, and can therefore be decorated by a variety of primary alcohols and amines, forming the necessary catalytic parts of the ribozyme, potentially reaching far more diversity than any amino acid protein scheme, simply by being much easier to synthesize or produce. Phosphate can also form hydrogen bonds with itself, bond metals and do a variety of things.

If the RNA world is left to evolve, potentialy making synthetic reactions before the ribosome can be made(which is a very narrow time scale), you would almost never get proteins to form, as the newly started compound synthesis quickly consumes any leftover primordial organic material and flushes the world with more hydrocarbons and saccirides.

These ribozymes could evolve further, using tRNA or equivalent to decorate the phosphate backbone of rna(think of how ribosomes on earth works), therefore making an extremely large and diverse family of molecules:

Bistable configurations that acts as switches and motors (proteins can’t do this), long hydrophobic sidechains that works like membranes (proteins can’t do this, again) and most importantly, the separation of form and function: decorated sidechains can be swapped out, forming multuple different enzymes while the rna sequence remains the same: when proteins have to reinvent the mill, ribozymes can just change tool tips.

There also exists a protein alternative: decorated polysaccharides, or enzymes made out of wood. Like peptides in proteins, saccirides are also stereochemically active, decoratable up to 3 positions on each ring by esterification or etherification by primary alcohols or carboxilic acids, can be linked in a way that encourage folding, and lastly, form complex internal hydrogen bond networks that stabilizes the complex and makes the polysaccharide structure both sophisticated and highly predictable: No more messing around with protein folding or thermodynamic minimums, just use dynamics.

Such biosphere would be alien to earth life: there would be no cells, as in a RNA world everything is done by the same molecule: rna forms the genetic material of living things, rna forms the machines that keeps them running, rna forms the part of the lifeforms that captures energy for it’s function, and rna will also form the structural elements, shells and skeletons of the lifeforms.

One added benefit of such arrangement is also that, unlike earth life, an advanced rna based organism can really evolve: there is an nearly infinite amount of possible molecular arrangements that are linked smoothly together by evolutionary bridges, unlike the tiny islands where proteins and earth life can almost never jump between. Biotechnology would be simple, as the computational complexity of predicting a dynamic based system like rna or polysaccharides is N^2 instead of the k^N of most thermodynamic based system like proteins. Which means rna life can be all crazy about how to make different usable stuff, directly out of their biology.

While earth life still struggle to make a few improvements with their flesh, trying hard to squeeze out the last bits of performance from their unpredictable and computationally costly proteins, lifeforms such like the prior mentionaned rna or sugar based life already has a 3D printer built into their bodies, by just choosing a simpler basic rule when they first came into being.

This is how being "penny wise and pound foolish" is spelled in biology.

$\begingroup$Just so you're aware, this has ended up in the low-quality queue, possibly because it's completely unreadable. You need to press enter twice for a paragraph break, not just once; I've gone ahead and fixed that for you.$\endgroup$
– F1KrazyJun 4 '18 at 15:43

$\begingroup$This is a pretty good answer, but you lost me at "there will be no cells"; even if RNA forms membranes... well, there are still membranes. And I see no reason why an advanced RNA world shouldn't still make use of lipids as well.$\endgroup$
– Logan R. KearsleyNov 12 '18 at 20:22

We know of no life forms that do not use proteins in some way so we cannot definitively answer that it is possible.

However there are a lot of universe out there and a lot of complex reactions possible. If other lifeforms did evolve then they may use something completely new - although they will need something that does the job of DNA and proteins even if it does it in a different way.

Note that life not even based on carbon has been suggested, for example Silicon based life forms. Again we don't know for sure what is possible but the chances that our way is the only way are fairly slim.

It might help if you understand more about what proteins actually do in the body. For reference, check out Wikipedia:

Proteins perform a vast array of functions within living organisms, including catalyzing metabolic reactions, DNA replication, responding to stimuli, and transporting molecules from one location to another.

Let's talk about catalyzing metabolic reactions. To use more simple terms, proteins make it possible for life to store and use energy.

Think about mountain climbers—their bodies have stored enough energy that they are able to climb up a mountain. If you look at a chart of energy densities, you'll see something interesting—fat has about the same energy density as the gasoline that you put in a car.

So why don't we burst into flame anytime we get close to a fire? Well, fat is a much less volatile form of energy storage, meaning it is more stable and much less likely to cause us to spontaneously combust. This also makes it harder to get energy out of it.

This is where we need a catalyst. In our bodies, proteins are the catalysts. They make it possible for our bodies to extract stored energy from fat in an easy and controlled way.

Just so you know, intelligence (even animal-level) requires a lot of energy. This means that unless the alien life in question is a mindless single-celled amoeba, it will need a reliable, safe source of energy.

So what would it take for a lifeform to not require proteins for this one specific purpose? As I just said, it will need a reliable and safe source of energy.

Imagine a (mostly) waterless planet that is tidally locked (one side is always facing the star it orbits). In addition, the distance between that planet and its star and the brightness of the sun is such that the day side of the planet is at the appropriate temperature for the life there.

Then, with constant sunlight and no clouds, it would not be necessary for life to store energy. Rather than going down the evolutionarily-costly process of develop proteins for catalyzing metabolic reactions, it could evolve to be more efficient at making use of the energy constantly being provided.

There are problems with this too, however. It would still be a significant advantage for something to have a larger energy store, as it would be able to spend more energy in a burst in order to catch prey or escape a predator. Also, I've only provided a way for a single use of proteins to become unnecessary.

In closing:

Hopefully looking a little closer at one particular use of proteins helps you understand just how useful they are to life. It is possible that alien life could be built around an entirely different biochemistry, such as silicon-based life. However, no matter what biochemistry is used I would expect there to be some protein analogue—they wouldn't look like the proteins we see on Earth, but they would perform the same kinds of functions as our proteins do.

Amino acids are a basic component of life. Even if you don't have them in a form that we know of, you would have to possess an analogous chemical structure.

Under different environmental conditions, life might evolve to work better with different chemical make ups than ours. So an organism that may be silicon based would probably have a structure that serves the function of an amino acid making up its body.